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- PDB-1vjf: CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FRO... -

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Basic information

Entry
Database: PDB / ID: 1vjf
TitleCRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION
ComponentsDNA-binding protein, putative
KeywordsDNA BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


aminoacyl-tRNA deacylase activity / DNA binding
Similarity search - Function
Prolyl-tRNA editing protein ProX/PRXD1 / YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein, putative
Similarity search - Component
Biological speciesCaulobacter crescentus CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative DNA-binding protein from Caulobacter crescentus at 1.62 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2514
Polymers20,0311
Non-polymers2203
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.891, 50.891, 121.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

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Components

#1: Protein DNA-binding protein, putative


Mass: 20031.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus CB15 (bacteria) / Species: Caulobacter vibrioides / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABV9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8
Details: 1.0M sodium citrate, 0.1M Tris pH 7.0, 0.2M NaCl, pH 7.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9796, 0.9794
DetectorType: ADSC / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97941
ReflectionResolution: 1.62→60.72 Å / Num. obs: 20981 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.41 Å2 / Rsym value: 0.059 / Net I/σ(I): 19.3
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1498 / Rsym value: 0.562 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0000refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→46.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.609 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16673 1077 5.1 %RANDOM
Rwork0.14488 ---
obs0.146 19865 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.62→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 13 172 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221350
X-RAY DIFFRACTIONr_bond_other_d0.0010.021282
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9561828
X-RAY DIFFRACTIONr_angle_other_deg0.81932977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74624.3158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.666157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02261
X-RAY DIFFRACTIONr_nbd_refined0.2180.2240
X-RAY DIFFRACTIONr_nbd_other0.1720.21233
X-RAY DIFFRACTIONr_nbtor_other0.0840.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.222
X-RAY DIFFRACTIONr_mcbond_it2.3753900
X-RAY DIFFRACTIONr_mcbond_other0.5413344
X-RAY DIFFRACTIONr_mcangle_it2.67851362
X-RAY DIFFRACTIONr_scbond_it4.4318541
X-RAY DIFFRACTIONr_scangle_it5.98911465
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 71 4.75 %
Rwork0.185 1424 -
Refinement TLS params.Method: refined / Origin x: 11.916 Å / Origin y: 9.972 Å / Origin z: 79.249 Å
111213212223313233
T-0.0695 Å20.0211 Å20.0086 Å2--0.0156 Å20.0178 Å2---0.0971 Å2
L1.5754 °2-0.128 °2-0.4375 °2-0.8905 °20.4608 °2--0.9649 °2
S-0.1337 Å °-0.1335 Å °-0.0419 Å °0.0789 Å °0.0699 Å °0.0422 Å °0.1249 Å °0.0921 Å °0.0638 Å °
Refinement TLS groupSelection: ALL

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